The Role of the Protein-Conducting Channel in the Membrane Insertion of Transmembrane Segments

Abstract

In all domains of life, the majority of membrane proteins are inserted into the membrane via a protein-conducting channel, also known as the SecY or Sec61 complex. In addition to a translocation pathway across the membrane, this channel features a unique lateral gate, which can open toward the membrane, permitting the sequential insertion of transmembrane segments (TMs). How this insertion occurs is still unclear, although a thermodynamic partioning between channel and membrane environments has been proposed. However, experiment- and simulation-based scales for the free-energy insertion cost of various amino acids differ, sometimes significantly as in the case of arginine (2-3 kcal/mol in experiment compared to 17 kcal/mol in simulation). Using free energy perturbation (FEP) simulations, we have calculated the insertion cost for an arginine located on a background poly-leucine helix, both in the center of a pure bilayer and in the center of a model of SecY featuring an open lateral gate. We find that the presence of SecY greatly reduces the membrane insertion cost for arginine, in agreement with prior simulations. We also consider the free energy cost for the insertion of the background helix from SecY to the membrane, which had been neglected previously.